## New names:
## Rows: 415 Columns: 4
## ── Column specification
## ──────────────────────────────────────────────────────── Delimiter: "\t" chr
## (1): ID dbl (3): Stromal_score, Immune_score, ESTIMATE_score
## ℹ Use `spec()` to retrieve the full column specification for this data. ℹ
## Specify the column types or set `show_col_types = FALSE` to quiet this message.
## • `SARIFA` -> `SARIFA...3`
## • `SARIFA` -> `SARIFA...4`
You can also embed plots, for example:
## [1] "Row names"
## [2] "ID"
## [3] "Stromal score"
## [4] "Immune score"
## [5] "ESTIMATE score"
## [6] "Row names y"
## [7] "sarifa group"
## [8] "barcode"
## [9] "patient"
## [10] "sample"
## [11] "shortLetterCode"
## [12] "definition"
## [13] "sample submitter id"
## [14] "sample type id"
## [15] "tumor descriptor"
## [16] "sample id"
## [17] "sample type"
## [18] "composition"
## [19] "days to collection"
## [20] "state"
## [21] "initial weight"
## [22] "intermediate dimension"
## [23] "pathology report uuid"
## [24] "submitter id"
## [25] "shortest dimension"
## [26] "oct embedded"
## [27] "longest dimension"
## [28] "is ffpe"
## [29] "tissue type"
## [30] "synchronous malignancy"
## [31] "ajcc pathologic stage"
## [32] "days to diagnosis"
## [33] "treatments"
## [34] "last known disease status"
## [35] "tissue or organ of origin"
## [36] "days to last follow up"
## [37] "age at diagnosis"
## [38] "primary diagnosis"
## [39] "prior malignancy"
## [40] "year of diagnosis"
## [41] "prior treatment"
## [42] "ajcc staging system edition"
## [43] "ajcc pathologic t"
## [44] "morphology"
## [45] "ajcc pathologic n"
## [46] "ajcc pathologic m"
## [47] "classification of tumor"
## [48] "diagnosis id"
## [49] "icd 10 code"
## [50] "site of resection or biopsy"
## [51] "tumor grade"
## [52] "progression or recurrence"
## [53] "alcohol history"
## [54] "exposure id"
## [55] "race"
## [56] "gender"
## [57] "ethnicity"
## [58] "vital status"
## [59] "age at index"
## [60] "days to birth"
## [61] "year of birth"
## [62] "demographic id"
## [63] "year of death"
## [64] "days to death"
## [65] "bcr patient barcode"
## [66] "primary site"
## [67] "project id"
## [68] "disease type"
## [69] "name"
## [70] "releasable"
## [71] "released"
## [72] "patient"
## [73] "Lauren Class"
## [74] "Intestinal Type Subclass"
## [75] "Signet Ring"
## [76] "WHO Class"
## [77] "Pathologic T"
## [78] "Pathologic N"
## [79] "Pathologic M"
## [80] "TNM Stage"
## [81] "Anatomic Region"
## [82] "Residual Tumor"
## [83] "Age at Initial Diagnosis"
## [84] "Country"
## [85] "Gender"
## [86] "Race"
## [87] "Vital Status"
## [88] "Days to Last Follow up"
## [89] "Days to Death"
## [90] "Recurrence"
## [91] "Days to Recurrence"
## [92] "Molecular Subtype"
## [93] "Total Mutation Rate"
## [94] "Hypermutated"
## [95] "MLH1 Epigenetically Silenced"
## [96] "CDKN2A Epigenetically Silenced"
## [97] "MSI status"
## [98] "EBV positive"
## [99] "TP53 mutation"
## [100] "PIK3CA mutation"
## [101] "KRAS mutation"
## [102] "ARID1A mutation"
## [103] "RHOA mutation"
## [104] "ARHGAP26 ARHGAP6 CLDN18 Rearrangement"
## [105] "MET Skipped Exon 2"
## [106] "MET Skipped Exons 18 and 19"
## [107] "ABSOLUTE Ploidy"
## [108] "ABSOLUTE Purity"
## [109] "Estimated Leukocyte Percentage"
## [110] "Percent Tumor Nuclei"
## [111] "Percent Tumor Cells"
## [112] "Percent Lymphocyte Infiltration"
## [113] "Gene Expression Cluster"
## [114] "MicroRNA Expression Cluster"
## [115] "Copy Number Cluster"
## [116] "Methylation Cluster"
## [117] "CIMP Category"
## [118] "stringAsFactor"
## [119] "sizeFactor"
## [120] "replaceable"
## [121] "Study ID"
## [122] "Kommentar"
## [123] "SARIFA 3"
## [124] "SARIFA 4"
## [125] "SARIFAreduziert"
## [126] "Sample ID"
## [127] "Diagnosis Age"
## [128] "Neoplasm Disease Stage American Joint Committee on Cancer Code"
## [129] "American Joint Committee on Cancer Publication Version Type"
## [130] "Aneuploidy Score"
## [131] "Cancer Type"
## [132] "TCGA PanCanAtlas Cancer Type Acronym"
## [133] "Cancer Type Detailed"
## [134] "Center of sequencing"
## [135] "Last Communication Contact from Initial Pathologic Diagnosis Date"
## [136] "Birth from Initial Pathologic Diagnosis Date"
## [137] "Last Alive Less Initial Pathologic Diagnosis Date Calculated Day Value"
## [138] "Disease Free (Months)"
## [139] "Disease Free Status"
## [140] "Months of disease-specific survival"
## [141] "Disease-specific Survival status"
## [142] "Ethnicity Category"
## [143] "Form completion date"
## [144] "Fraction Genome Altered"
## [145] "Neoplasm Histologic Grade"
## [146] "Neoadjuvant Therapy Type Administered Prior To Resection Text"
## [147] "ICD-10 Classification"
## [148] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code"
## [149] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code"
## [150] "Informed consent verified"
## [151] "In PanCan Pathway Analysis"
## [152] "MSI MANTIS Score"
## [153] "MSIsensor Score"
## [154] "Mutation Count"
## [155] "New Neoplasm Event Post Initial Therapy Indicator"
## [156] "Oncotree Code"
## [157] "Overall Survival (Months)"
## [158] "Overall Survival Status"
## [159] "Other Patient ID"
## [160] "American Joint Committee on Cancer Metastasis Stage Code"
## [161] "Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code"
## [162] "American Joint Committee on Cancer Tumor Stage Code"
## [163] "Person Neoplasm Cancer Status"
## [164] "Progress Free Survival (Months)"
## [165] "Progression Free Status"
## [166] "Primary Lymph Node Presentation Assessment"
## [167] "Prior Diagnosis"
## [168] "Race Category"
## [169] "Radiation Therapy"
## [170] "Number of Samples Per Patient"
## [171] "Sample Type"
## [172] "Sex"
## [173] "Somatic Status"
## [174] "Subtype"
## [175] "Tissue Prospective Collection Indicator"
## [176] "Tissue Retrospective Collection Indicator"
## [177] "Tissue Source Site"
## [178] "TMB (nonsynonymous)"
## [179] "Tumor Disease Anatomic Site"
## [180] "Tumor Type"
## [181] "Patient Weight"
## [1] "Row names"
## [2] "ID"
## [3] "Stromal score"
## [4] "Immune score"
## [5] "ESTIMATE score"
## [6] "Row names y"
## [7] "sarifa group"
## [8] "barcode"
## [9] "patient"
## [10] "sample"
## [11] "shortLetterCode"
## [12] "definition"
## [13] "sample submitter id"
## [14] "sample type id"
## [15] "tumor descriptor"
## [16] "sample id"
## [17] "sample type"
## [18] "composition"
## [19] "days to collection"
## [20] "state"
## [21] "initial weight"
## [22] "intermediate dimension"
## [23] "pathology report uuid"
## [24] "submitter id"
## [25] "shortest dimension"
## [26] "oct embedded"
## [27] "longest dimension"
## [28] "is ffpe"
## [29] "tissue type"
## [30] "synchronous malignancy"
## [31] "ajcc pathologic stage"
## [32] "days to diagnosis"
## [33] "treatments"
## [34] "last known disease status"
## [35] "tissue or organ of origin"
## [36] "days to last follow up"
## [37] "age at diagnosis"
## [38] "primary diagnosis"
## [39] "prior malignancy"
## [40] "year of diagnosis"
## [41] "prior treatment"
## [42] "ajcc staging system edition"
## [43] "ajcc pathologic t"
## [44] "morphology"
## [45] "ajcc pathologic n"
## [46] "ajcc pathologic m"
## [47] "classification of tumor"
## [48] "diagnosis id"
## [49] "icd 10 code"
## [50] "site of resection or biopsy"
## [51] "tumor grade"
## [52] "progression or recurrence"
## [53] "alcohol history"
## [54] "exposure id"
## [55] "race"
## [56] "gender"
## [57] "ethnicity"
## [58] "vital status"
## [59] "age at index"
## [60] "days to birth"
## [61] "year of birth"
## [62] "demographic id"
## [63] "year of death"
## [64] "days to death"
## [65] "bcr patient barcode"
## [66] "primary site"
## [67] "project id"
## [68] "disease type"
## [69] "name"
## [70] "releasable"
## [71] "released"
## [72] "patient"
## [73] "Lauren Class"
## [74] "Intestinal Type Subclass"
## [75] "Signet Ring"
## [76] "WHO Class"
## [77] "Pathologic T"
## [78] "Pathologic N"
## [79] "Pathologic M"
## [80] "TNM Stage"
## [81] "Anatomic Region"
## [82] "Residual Tumor"
## [83] "Age at Initial Diagnosis"
## [84] "Country"
## [85] "Gender"
## [86] "Race"
## [87] "Vital Status"
## [88] "Days to Last Follow up"
## [89] "Days to Death"
## [90] "Recurrence"
## [91] "Days to Recurrence"
## [92] "Molecular Subtype"
## [93] "Total Mutation Rate"
## [94] "Hypermutated"
## [95] "MLH1 Epigenetically Silenced"
## [96] "CDKN2A Epigenetically Silenced"
## [97] "MSI status"
## [98] "EBV positive"
## [99] "TP53 mutation"
## [100] "PIK3CA mutation"
## [101] "KRAS mutation"
## [102] "ARID1A mutation"
## [103] "RHOA mutation"
## [104] "ARHGAP26 ARHGAP6 CLDN18 Rearrangement"
## [105] "MET Skipped Exon 2"
## [106] "MET Skipped Exons 18 and 19"
## [107] "ABSOLUTE Ploidy"
## [108] "ABSOLUTE Purity"
## [109] "Estimated Leukocyte Percentage"
## [110] "Percent Tumor Nuclei"
## [111] "Percent Tumor Cells"
## [112] "Percent Lymphocyte Infiltration"
## [113] "Gene Expression Cluster"
## [114] "MicroRNA Expression Cluster"
## [115] "Copy Number Cluster"
## [116] "Methylation Cluster"
## [117] "CIMP Category"
## [118] "stringAsFactor"
## [119] "sizeFactor"
## [120] "replaceable"
## [121] "Study ID"
## [122] "Kommentar"
## [123] "SARIFA 3"
## [124] "SARIFA 4"
## [125] "SARIFAreduziert"
## [126] "Sample ID"
## [127] "Diagnosis Age"
## [128] "Neoplasm Disease Stage American Joint Committee on Cancer Code"
## [129] "American Joint Committee on Cancer Publication Version Type"
## [130] "Aneuploidy Score"
## [131] "Cancer Type"
## [132] "TCGA PanCanAtlas Cancer Type Acronym"
## [133] "Cancer Type Detailed"
## [134] "Center of sequencing"
## [135] "Last Communication Contact from Initial Pathologic Diagnosis Date"
## [136] "Birth from Initial Pathologic Diagnosis Date"
## [137] "Last Alive Less Initial Pathologic Diagnosis Date Calculated Day Value"
## [138] "Disease Free (Months)"
## [139] "Disease Free Status"
## [140] "Months of disease-specific survival"
## [141] "Disease-specific Survival status"
## [142] "Ethnicity Category"
## [143] "Form completion date"
## [144] "Fraction Genome Altered"
## [145] "Neoplasm Histologic Grade"
## [146] "Neoadjuvant Therapy Type Administered Prior To Resection Text"
## [147] "ICD-10 Classification"
## [148] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code"
## [149] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code"
## [150] "Informed consent verified"
## [151] "In PanCan Pathway Analysis"
## [152] "MSI MANTIS Score"
## [153] "MSIsensor Score"
## [154] "Mutation Count"
## [155] "New Neoplasm Event Post Initial Therapy Indicator"
## [156] "Oncotree Code"
## [157] "Overall Survival (Months)"
## [158] "Overall Survival Status"
## [159] "Other Patient ID"
## [160] "American Joint Committee on Cancer Metastasis Stage Code"
## [161] "Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code"
## [162] "American Joint Committee on Cancer Tumor Stage Code"
## [163] "Person Neoplasm Cancer Status"
## [164] "Progress Free Survival (Months)"
## [165] "Progression Free Status"
## [166] "Primary Lymph Node Presentation Assessment"
## [167] "Prior Diagnosis"
## [168] "Race Category"
## [169] "Radiation Therapy"
## [170] "Number of Samples Per Patient"
## [171] "Sample Type"
## [172] "Sex"
## [173] "Somatic Status"
## [174] "Subtype"
## [175] "Tissue Prospective Collection Indicator"
## [176] "Tissue Retrospective Collection Indicator"
## [177] "Tissue Source Site"
## [178] "TMB (nonsynonymous)"
## [179] "Tumor Disease Anatomic Site"
## [180] "Tumor Type"
## [181] "Patient Weight"
## [1] "Row names"
## [2] "ID"
## [3] "Stromal score"
## [4] "Immune score"
## [5] "ESTIMATE score"
## [6] "Row names y"
## [7] "sarifa group"
## [8] "barcode"
## [9] "patient"
## [10] "sample"
## [11] "shortLetterCode"
## [12] "definition"
## [13] "sample submitter id"
## [14] "sample type id"
## [15] "tumor descriptor"
## [16] "sample id"
## [17] "sample type"
## [18] "composition"
## [19] "days to collection"
## [20] "state"
## [21] "initial weight"
## [22] "intermediate dimension"
## [23] "pathology report uuid"
## [24] "submitter id"
## [25] "shortest dimension"
## [26] "oct embedded"
## [27] "longest dimension"
## [28] "is ffpe"
## [29] "tissue type"
## [30] "synchronous malignancy"
## [31] "ajcc pathologic stage"
## [32] "days to diagnosis"
## [33] "treatments"
## [34] "last known disease status"
## [35] "tissue or organ of origin"
## [36] "days to last follow up"
## [37] "age at diagnosis"
## [38] "primary diagnosis"
## [39] "prior malignancy"
## [40] "year of diagnosis"
## [41] "prior treatment"
## [42] "ajcc staging system edition"
## [43] "ajcc pathologic t"
## [44] "morphology"
## [45] "ajcc pathologic n"
## [46] "ajcc pathologic m"
## [47] "classification of tumor"
## [48] "diagnosis id"
## [49] "icd 10 code"
## [50] "site of resection or biopsy"
## [51] "tumor grade"
## [52] "progression or recurrence"
## [53] "alcohol history"
## [54] "exposure id"
## [55] "race"
## [56] "gender"
## [57] "ethnicity"
## [58] "vital status"
## [59] "age at index"
## [60] "days to birth"
## [61] "year of birth"
## [62] "demographic id"
## [63] "year of death"
## [64] "days to death"
## [65] "bcr patient barcode"
## [66] "primary site"
## [67] "project id"
## [68] "disease type"
## [69] "name"
## [70] "releasable"
## [71] "released"
## [72] "patient"
## [73] "Lauren Class"
## [74] "Intestinal Type Subclass"
## [75] "Signet Ring"
## [76] "WHO Class"
## [77] "Pathologic T"
## [78] "Pathologic N"
## [79] "Pathologic M"
## [80] "TNM Stage"
## [81] "Anatomic Region"
## [82] "Residual Tumor"
## [83] "Age at Initial Diagnosis"
## [84] "Country"
## [85] "Gender"
## [86] "Race"
## [87] "Vital Status"
## [88] "Days to Last Follow up"
## [89] "Days to Death"
## [90] "Recurrence"
## [91] "Days to Recurrence"
## [92] "Molecular Subtype"
## [93] "Total Mutation Rate"
## [94] "Hypermutated"
## [95] "MLH1 Epigenetically Silenced"
## [96] "CDKN2A Epigenetically Silenced"
## [97] "MSI status"
## [98] "EBV positive"
## [99] "TP53 mutation"
## [100] "PIK3CA mutation"
## [101] "KRAS mutation"
## [102] "ARID1A mutation"
## [103] "RHOA mutation"
## [104] "ARHGAP26 ARHGAP6 CLDN18 Rearrangement"
## [105] "MET Skipped Exon 2"
## [106] "MET Skipped Exons 18 and 19"
## [107] "ABSOLUTE Ploidy"
## [108] "ABSOLUTE Purity"
## [109] "Estimated Leukocyte Percentage"
## [110] "Percent Tumor Nuclei"
## [111] "Percent Tumor Cells"
## [112] "Percent Lymphocyte Infiltration"
## [113] "Gene Expression Cluster"
## [114] "MicroRNA Expression Cluster"
## [115] "Copy Number Cluster"
## [116] "Methylation Cluster"
## [117] "CIMP Category"
## [118] "stringAsFactor"
## [119] "sizeFactor"
## [120] "replaceable"
## [121] "Study ID"
## [122] "Kommentar"
## [123] "SARIFA 3"
## [124] "SARIFA 4"
## [125] "SARIFAreduziert"
## [126] "Sample ID"
## [127] "Diagnosis Age"
## [128] "Neoplasm Disease Stage American Joint Committee on Cancer Code"
## [129] "American Joint Committee on Cancer Publication Version Type"
## [130] "Aneuploidy Score"
## [131] "Cancer Type"
## [132] "TCGA PanCanAtlas Cancer Type Acronym"
## [133] "Cancer Type Detailed"
## [134] "Center of sequencing"
## [135] "Last Communication Contact from Initial Pathologic Diagnosis Date"
## [136] "Birth from Initial Pathologic Diagnosis Date"
## [137] "Last Alive Less Initial Pathologic Diagnosis Date Calculated Day Value"
## [138] "Disease Free (Months)"
## [139] "Disease Free Status"
## [140] "Months of disease-specific survival"
## [141] "Disease-specific Survival status"
## [142] "Ethnicity Category"
## [143] "Form completion date"
## [144] "Fraction Genome Altered"
## [145] "Neoplasm Histologic Grade"
## [146] "Neoadjuvant Therapy Type Administered Prior To Resection Text"
## [147] "ICD-10 Classification"
## [148] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code"
## [149] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code"
## [150] "Informed consent verified"
## [151] "In PanCan Pathway Analysis"
## [152] "MSI MANTIS Score"
## [153] "MSIsensor Score"
## [154] "Mutation Count"
## [155] "New Neoplasm Event Post Initial Therapy Indicator"
## [156] "Oncotree Code"
## [157] "Overall Survival (Months)"
## [158] "Overall Survival Status"
## [159] "Other Patient ID"
## [160] "American Joint Committee on Cancer Metastasis Stage Code"
## [161] "Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code"
## [162] "American Joint Committee on Cancer Tumor Stage Code"
## [163] "Person Neoplasm Cancer Status"
## [164] "Progress Free Survival (Months)"
## [165] "Progression Free Status"
## [166] "Primary Lymph Node Presentation Assessment"
## [167] "Prior Diagnosis"
## [168] "Race Category"
## [169] "Radiation Therapy"
## [170] "Number of Samples Per Patient"
## [171] "Sample Type"
## [172] "Sex"
## [173] "Somatic Status"
## [174] "Subtype"
## [175] "Tissue Prospective Collection Indicator"
## [176] "Tissue Retrospective Collection Indicator"
## [177] "Tissue Source Site"
## [178] "TMB (nonsynonymous)"
## [179] "Tumor Disease Anatomic Site"
## [180] "Tumor Type"
## [181] "Patient Weight"
## [1] "Row names"
## [2] "ID"
## [3] "Stromal score"
## [4] "Immune score"
## [5] "ESTIMATE score"
## [6] "Row names y"
## [7] "sarifa group"
## [8] "barcode"
## [9] "patient"
## [10] "sample"
## [11] "shortLetterCode"
## [12] "definition"
## [13] "sample submitter id"
## [14] "sample type id"
## [15] "tumor descriptor"
## [16] "sample id"
## [17] "sample type"
## [18] "composition"
## [19] "days to collection"
## [20] "state"
## [21] "initial weight"
## [22] "intermediate dimension"
## [23] "pathology report uuid"
## [24] "submitter id"
## [25] "shortest dimension"
## [26] "oct embedded"
## [27] "longest dimension"
## [28] "is ffpe"
## [29] "tissue type"
## [30] "synchronous malignancy"
## [31] "ajcc pathologic stage"
## [32] "days to diagnosis"
## [33] "treatments"
## [34] "last known disease status"
## [35] "tissue or organ of origin"
## [36] "days to last follow up"
## [37] "age at diagnosis"
## [38] "primary diagnosis"
## [39] "prior malignancy"
## [40] "year of diagnosis"
## [41] "prior treatment"
## [42] "ajcc staging system edition"
## [43] "ajcc pathologic t"
## [44] "morphology"
## [45] "ajcc pathologic n"
## [46] "ajcc pathologic m"
## [47] "classification of tumor"
## [48] "diagnosis id"
## [49] "icd 10 code"
## [50] "site of resection or biopsy"
## [51] "tumor grade"
## [52] "progression or recurrence"
## [53] "alcohol history"
## [54] "exposure id"
## [55] "race"
## [56] "gender"
## [57] "ethnicity"
## [58] "vital status"
## [59] "age at index"
## [60] "days to birth"
## [61] "year of birth"
## [62] "demographic id"
## [63] "year of death"
## [64] "days to death"
## [65] "bcr patient barcode"
## [66] "primary site"
## [67] "project id"
## [68] "disease type"
## [69] "name"
## [70] "releasable"
## [71] "released"
## [72] "patient"
## [73] "Lauren Class"
## [74] "Intestinal Type Subclass"
## [75] "Signet Ring"
## [76] "WHO Class"
## [77] "Pathologic T"
## [78] "Pathologic N"
## [79] "Pathologic M"
## [80] "TNM Stage"
## [81] "Anatomic Region"
## [82] "Residual Tumor"
## [83] "Age at Initial Diagnosis"
## [84] "Country"
## [85] "Gender"
## [86] "Race"
## [87] "Vital Status"
## [88] "Days to Last Follow up"
## [89] "Days to Death"
## [90] "Recurrence"
## [91] "Days to Recurrence"
## [92] "Molecular Subtype"
## [93] "Total Mutation Rate"
## [94] "Hypermutated"
## [95] "MLH1 Epigenetically Silenced"
## [96] "CDKN2A Epigenetically Silenced"
## [97] "MSI status"
## [98] "EBV positive"
## [99] "TP53 mutation"
## [100] "PIK3CA mutation"
## [101] "KRAS mutation"
## [102] "ARID1A mutation"
## [103] "RHOA mutation"
## [104] "ARHGAP26 ARHGAP6 CLDN18 Rearrangement"
## [105] "MET Skipped Exon 2"
## [106] "MET Skipped Exons 18 and 19"
## [107] "ABSOLUTE Ploidy"
## [108] "ABSOLUTE Purity"
## [109] "Estimated Leukocyte Percentage"
## [110] "Percent Tumor Nuclei"
## [111] "Percent Tumor Cells"
## [112] "Percent Lymphocyte Infiltration"
## [113] "Gene Expression Cluster"
## [114] "MicroRNA Expression Cluster"
## [115] "Copy Number Cluster"
## [116] "Methylation Cluster"
## [117] "CIMP Category"
## [118] "stringAsFactor"
## [119] "sizeFactor"
## [120] "replaceable"
## [121] "Study ID"
## [122] "Kommentar"
## [123] "SARIFA 3"
## [124] "SARIFA 4"
## [125] "SARIFAreduziert"
## [126] "Sample ID"
## [127] "Diagnosis Age"
## [128] "Neoplasm Disease Stage American Joint Committee on Cancer Code"
## [129] "American Joint Committee on Cancer Publication Version Type"
## [130] "Aneuploidy Score"
## [131] "Cancer Type"
## [132] "TCGA PanCanAtlas Cancer Type Acronym"
## [133] "Cancer Type Detailed"
## [134] "Center of sequencing"
## [135] "Last Communication Contact from Initial Pathologic Diagnosis Date"
## [136] "Birth from Initial Pathologic Diagnosis Date"
## [137] "Last Alive Less Initial Pathologic Diagnosis Date Calculated Day Value"
## [138] "Disease Free (Months)"
## [139] "Disease Free Status"
## [140] "Months of disease-specific survival"
## [141] "Disease-specific Survival status"
## [142] "Ethnicity Category"
## [143] "Form completion date"
## [144] "Fraction Genome Altered"
## [145] "Neoplasm Histologic Grade"
## [146] "Neoadjuvant Therapy Type Administered Prior To Resection Text"
## [147] "ICD-10 Classification"
## [148] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Histology Code"
## [149] "International Classification of Diseases for Oncology, Third Edition ICD-O-3 Site Code"
## [150] "Informed consent verified"
## [151] "In PanCan Pathway Analysis"
## [152] "MSI MANTIS Score"
## [153] "MSIsensor Score"
## [154] "Mutation Count"
## [155] "New Neoplasm Event Post Initial Therapy Indicator"
## [156] "Oncotree Code"
## [157] "Overall Survival (Months)"
## [158] "Overall Survival Status"
## [159] "Other Patient ID"
## [160] "American Joint Committee on Cancer Metastasis Stage Code"
## [161] "Neoplasm Disease Lymph Node Stage American Joint Committee on Cancer Code"
## [162] "American Joint Committee on Cancer Tumor Stage Code"
## [163] "Person Neoplasm Cancer Status"
## [164] "Progress Free Survival (Months)"
## [165] "Progression Free Status"
## [166] "Primary Lymph Node Presentation Assessment"
## [167] "Prior Diagnosis"
## [168] "Race Category"
## [169] "Radiation Therapy"
## [170] "Number of Samples Per Patient"
## [171] "Sample Type"
## [172] "Sex"
## [173] "Somatic Status"
## [174] "Subtype"
## [175] "Tissue Prospective Collection Indicator"
## [176] "Tissue Retrospective Collection Indicator"
## [177] "Tissue Source Site"
## [178] "TMB (nonsynonymous)"
## [179] "Tumor Disease Anatomic Site"
## [180] "Tumor Type"
## [181] "Patient Weight"
## The automatically generated colors map from the minus and plus 99^th of
## the absolute values in the matrix. There are outliers in the matrix
## whose patterns might be hidden by this color mapping. You can manually
## set the color to `col` argument.
##
## Use `suppressMessages()` to turn off this message.
## `geom_smooth()` using formula = 'y ~ x'
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## preparing geneSet collections...
## GSEA analysis...
## leading edge analysis...
## done...
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
To check whether SARIFA is associated with processes paired with immune cell infiltration data from TIMER https://academic.oup.com/nar/article/48/W1/W509/5842187?login=true
## New names:
## Rows: 11070 Columns: 120
## ── Column specification
## ──────────────────────────────────────────────────────── Delimiter: "," chr
## (1): cell_type dbl (119): B.cell_TIMER, T.cell.CD4._TIMER, T.cell.CD8._TIMER,
## Neutrophil_TI...
## ℹ Use `spec()` to retrieve the full column specification for this data. ℹ
## Specify the column types or set `show_col_types = FALSE` to quiet this message.
## • `B cell_TIMER` -> `B.cell_TIMER`
## • `T cell CD4+_TIMER` -> `T.cell.CD4._TIMER`
## • `T cell CD8+_TIMER` -> `T.cell.CD8._TIMER`
## • `Myeloid dendritic cell_TIMER` -> `Myeloid.dendritic.cell_TIMER`
## • `B cell naive_CIBERSORT` -> `B.cell.naive_CIBERSORT`
## • `B cell memory_CIBERSORT` -> `B.cell.memory_CIBERSORT`
## • `B cell plasma_CIBERSORT` -> `B.cell.plasma_CIBERSORT`
## • `T cell CD8+_CIBERSORT` -> `T.cell.CD8._CIBERSORT`
## • `T cell CD4+ naive_CIBERSORT` -> `T.cell.CD4..naive_CIBERSORT`
## • `T cell CD4+ memory resting_CIBERSORT` ->
## `T.cell.CD4..memory.resting_CIBERSORT`
## • `T cell CD4+ memory activated_CIBERSORT` ->
## `T.cell.CD4..memory.activated_CIBERSORT`
## • `T cell follicular helper_CIBERSORT` -> `T.cell.follicular.helper_CIBERSORT`
## • `T cell regulatory (Tregs)_CIBERSORT` ->
## `T.cell.regulatory..Tregs._CIBERSORT`
## • `T cell gamma delta_CIBERSORT` -> `T.cell.gamma.delta_CIBERSORT`
## • `NK cell resting_CIBERSORT` -> `NK.cell.resting_CIBERSORT`
## • `NK cell activated_CIBERSORT` -> `NK.cell.activated_CIBERSORT`
## • `Macrophage M0_CIBERSORT` -> `Macrophage.M0_CIBERSORT`
## • `Macrophage M1_CIBERSORT` -> `Macrophage.M1_CIBERSORT`
## • `Macrophage M2_CIBERSORT` -> `Macrophage.M2_CIBERSORT`
## • `Myeloid dendritic cell resting_CIBERSORT` ->
## `Myeloid.dendritic.cell.resting_CIBERSORT`
## • `Myeloid dendritic cell activated_CIBERSORT` ->
## `Myeloid.dendritic.cell.activated_CIBERSORT`
## • `Mast cell activated_CIBERSORT` -> `Mast.cell.activated_CIBERSORT`
## • `Mast cell resting_CIBERSORT` -> `Mast.cell.resting_CIBERSORT`
## • `B cell naive_CIBERSORT-ABS` -> `B.cell.naive_CIBERSORT.ABS`
## • `B cell memory_CIBERSORT-ABS` -> `B.cell.memory_CIBERSORT.ABS`
## • `B cell plasma_CIBERSORT-ABS` -> `B.cell.plasma_CIBERSORT.ABS`
## • `T cell CD8+_CIBERSORT-ABS` -> `T.cell.CD8._CIBERSORT.ABS`
## • `T cell CD4+ naive_CIBERSORT-ABS` -> `T.cell.CD4..naive_CIBERSORT.ABS`
## • `T cell CD4+ memory resting_CIBERSORT-ABS` ->
## `T.cell.CD4..memory.resting_CIBERSORT.ABS`
## • `T cell CD4+ memory activated_CIBERSORT-ABS` ->
## `T.cell.CD4..memory.activated_CIBERSORT.ABS`
## • `T cell follicular helper_CIBERSORT-ABS` ->
## `T.cell.follicular.helper_CIBERSORT.ABS`
## • `T cell regulatory (Tregs)_CIBERSORT-ABS` ->
## `T.cell.regulatory..Tregs._CIBERSORT.ABS`
## • `T cell gamma delta_CIBERSORT-ABS` -> `T.cell.gamma.delta_CIBERSORT.ABS`
## • `NK cell resting_CIBERSORT-ABS` -> `NK.cell.resting_CIBERSORT.ABS`
## • `NK cell activated_CIBERSORT-ABS` -> `NK.cell.activated_CIBERSORT.ABS`
## • `Monocyte_CIBERSORT-ABS` -> `Monocyte_CIBERSORT.ABS`
## • `Macrophage M0_CIBERSORT-ABS` -> `Macrophage.M0_CIBERSORT.ABS`
## • `Macrophage M1_CIBERSORT-ABS` -> `Macrophage.M1_CIBERSORT.ABS`
## • `Macrophage M2_CIBERSORT-ABS` -> `Macrophage.M2_CIBERSORT.ABS`
## • `Myeloid dendritic cell resting_CIBERSORT-ABS` ->
## `Myeloid.dendritic.cell.resting_CIBERSORT.ABS`
## • `Myeloid dendritic cell activated_CIBERSORT-ABS` ->
## `Myeloid.dendritic.cell.activated_CIBERSORT.ABS`
## • `Mast cell activated_CIBERSORT-ABS` -> `Mast.cell.activated_CIBERSORT.ABS`
## • `Mast cell resting_CIBERSORT-ABS` -> `Mast.cell.resting_CIBERSORT.ABS`
## • `Eosinophil_CIBERSORT-ABS` -> `Eosinophil_CIBERSORT.ABS`
## • `Neutrophil_CIBERSORT-ABS` -> `Neutrophil_CIBERSORT.ABS`
## • `B cell_QUANTISEQ` -> `B.cell_QUANTISEQ`
## • `Macrophage M1_QUANTISEQ` -> `Macrophage.M1_QUANTISEQ`
## • `Macrophage M2_QUANTISEQ` -> `Macrophage.M2_QUANTISEQ`
## • `NK cell_QUANTISEQ` -> `NK.cell_QUANTISEQ`
## • `T cell CD4+ (non-regulatory)_QUANTISEQ` ->
## `T.cell.CD4...non.regulatory._QUANTISEQ`
## • `T cell CD8+_QUANTISEQ` -> `T.cell.CD8._QUANTISEQ`
## • `T cell regulatory (Tregs)_QUANTISEQ` ->
## `T.cell.regulatory..Tregs._QUANTISEQ`
## • `Myeloid dendritic cell_QUANTISEQ` -> `Myeloid.dendritic.cell_QUANTISEQ`
## • `uncharacterized cell_QUANTISEQ` -> `uncharacterized.cell_QUANTISEQ`
## • `T cell_MCPCOUNTER` -> `T.cell_MCPCOUNTER`
## • `T cell CD8+_MCPCOUNTER` -> `T.cell.CD8._MCPCOUNTER`
## • `cytotoxicity score_MCPCOUNTER` -> `cytotoxicity.score_MCPCOUNTER`
## • `NK cell_MCPCOUNTER` -> `NK.cell_MCPCOUNTER`
## • `B cell_MCPCOUNTER` -> `B.cell_MCPCOUNTER`
## • `Macrophage/Monocyte_MCPCOUNTER` -> `Macrophage.Monocyte_MCPCOUNTER`
## • `Myeloid dendritic cell_MCPCOUNTER` -> `Myeloid.dendritic.cell_MCPCOUNTER`
## • `Endothelial cell_MCPCOUNTER` -> `Endothelial.cell_MCPCOUNTER`
## • `Cancer associated fibroblast_MCPCOUNTER` ->
## `Cancer.associated.fibroblast_MCPCOUNTER`
## • `Myeloid dendritic cell activated_XCELL` ->
## `Myeloid.dendritic.cell.activated_XCELL`
## • `B cell_XCELL` -> `B.cell_XCELL`
## • `T cell CD4+ memory_XCELL` -> `T.cell.CD4..memory_XCELL`
## • `T cell CD4+ naive_XCELL` -> `T.cell.CD4..naive_XCELL`
## • `T cell CD4+ (non-regulatory)_XCELL` -> `T.cell.CD4...non.regulatory._XCELL`
## • `T cell CD4+ central memory_XCELL` -> `T.cell.CD4..central.memory_XCELL`
## • `T cell CD4+ effector memory_XCELL` -> `T.cell.CD4..effector.memory_XCELL`
## • `T cell CD8+ naive_XCELL` -> `T.cell.CD8..naive_XCELL`
## • `T cell CD8+_XCELL` -> `T.cell.CD8._XCELL`
## • `T cell CD8+ central memory_XCELL` -> `T.cell.CD8..central.memory_XCELL`
## • `T cell CD8+ effector memory_XCELL` -> `T.cell.CD8..effector.memory_XCELL`
## • `Class-switched memory B cell_XCELL` -> `Class.switched.memory.B.cell_XCELL`
## • `Common lymphoid progenitor_XCELL` -> `Common.lymphoid.progenitor_XCELL`
## • `Common myeloid progenitor_XCELL` -> `Common.myeloid.progenitor_XCELL`
## • `Myeloid dendritic cell_XCELL` -> `Myeloid.dendritic.cell_XCELL`
## • `Endothelial cell_XCELL` -> `Endothelial.cell_XCELL`
## • `Cancer associated fibroblast_XCELL` -> `Cancer.associated.fibroblast_XCELL`
## • `Granulocyte-monocyte progenitor_XCELL` ->
## `Granulocyte.monocyte.progenitor_XCELL`
## • `Hematopoietic stem cell_XCELL` -> `Hematopoietic.stem.cell_XCELL`
## • `Macrophage M1_XCELL` -> `Macrophage.M1_XCELL`
## • `Macrophage M2_XCELL` -> `Macrophage.M2_XCELL`
## • `Mast cell_XCELL` -> `Mast.cell_XCELL`
## • `B cell memory_XCELL` -> `B.cell.memory_XCELL`
## • `B cell naive_XCELL` -> `B.cell.naive_XCELL`
## • `NK cell_XCELL` -> `NK.cell_XCELL`
## • `T cell NK_XCELL` -> `T.cell.NK_XCELL`
## • `Plasmacytoid dendritic cell_XCELL` -> `Plasmacytoid.dendritic.cell_XCELL`
## • `B cell plasma_XCELL` -> `B.cell.plasma_XCELL`
## • `T cell gamma delta_XCELL` -> `T.cell.gamma.delta_XCELL`
## • `T cell CD4+ Th1_XCELL` -> `T.cell.CD4..Th1_XCELL`
## • `T cell CD4+ Th2_XCELL` -> `T.cell.CD4..Th2_XCELL`
## • `T cell regulatory (Tregs)_XCELL` -> `T.cell.regulatory..Tregs._XCELL`
## • `immune score_XCELL` -> `immune.score_XCELL`
## • `stroma score_XCELL` -> `stroma.score_XCELL`
## • `microenvironment score_XCELL` -> `microenvironment.score_XCELL`
## • `B cell_EPIC` -> `B.cell_EPIC`
## • `Cancer associated fibroblast_EPIC` -> `Cancer.associated.fibroblast_EPIC`
## • `T cell CD4+_EPIC` -> `T.cell.CD4._EPIC`
## • `T cell CD8+_EPIC` -> `T.cell.CD8._EPIC`
## • `Endothelial cell_EPIC` -> `Endothelial.cell_EPIC`
## • `NK cell_EPIC` -> `NK.cell_EPIC`
## • `uncharacterized cell_EPIC` -> `uncharacterized.cell_EPIC`
## Rows: 6475 Columns: 88
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (16): TCGA_ID, Sex, Histology, Tissue, B.cells_state_assignments, CD4.T....
## dbl (72): B.cells_S01, B.cells_S02, B.cells_S03, B.cells_S04, B.cells_S05, B...
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Here we analyze the PCA plots from SARIFA for their activitiy
## -- removing the lower 50% of variables based on variance
## Rows: 22584 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (6): Gene, Cytoband, (A) NON-SARIFA, (B) SARIFA, Log Ratio, Enriched in
## dbl (2): p-Value, q-Value
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Saving 8 x 6 in image
## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
## `geom_smooth()` using formula = 'y ~ x'